A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-11-21, 11:25 EST
based on data in:
/gpfs/projects/GenomicsCore/BGE510
General Statistics
| Sample Name | Duplication | % Aligned | M Aligned | Library types | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | % Duplication | % > Q30 | Mb Q30 bases | Reads After Filtering | GC content | % PF | % Adapter |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR5448113 | 7.7% | 100.0% | 4.2M | IU | 4.8M | 4.7M | 98.0% | 4.3M | 87.9% | 0.5M | |||||||
| SRR5448113_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 88.0% | 0.5M | |||||||||||
| SRR5448113_subsample_1 | 4.5% | 97.9% | 479.2Mb | 9.7M | 50.3% | 96.7% | 0.2% | ||||||||||
| SRR5448114 | 6.6% | 100.0% | 4.3M | IU | 4.8M | 4.7M | 97.9% | 4.3M | 88.5% | 0.5M | |||||||
| SRR5448114_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 88.5% | 0.5M | |||||||||||
| SRR5448114_subsample_1 | 3.8% | 97.8% | 479.3Mb | 9.7M | 50.4% | 96.7% | 0.2% | ||||||||||
| SRR5448115 | 7.9% | 100.0% | 4.2M | IU | 4.8M | 4.7M | 97.9% | 4.2M | 87.8% | 0.5M | |||||||
| SRR5448115_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 87.8% | 0.5M | |||||||||||
| SRR5448115_subsample_1 | 4.7% | 97.9% | 479.6Mb | 9.7M | 50.3% | 96.8% | 0.2% | ||||||||||
| SRR5448116 | 7.2% | 100.0% | 4.3M | IU | 4.8M | 4.7M | 98.0% | 4.3M | 88.8% | 0.4M | |||||||
| SRR5448116_STARpass1 | 4.8M | 4.7M | 98.0% | 4.3M | 88.8% | 0.4M | |||||||||||
| SRR5448116_subsample_1 | 4.2% | 97.9% | 478.5Mb | 9.7M | 50.5% | 96.6% | 0.2% | ||||||||||
| SRR5448117 | 7.5% | 100.0% | 4.2M | IU | 4.8M | 4.7M | 97.8% | 4.3M | 88.2% | 0.5M | |||||||
| SRR5448117_STARpass1 | 4.8M | 4.7M | 97.8% | 4.3M | 88.2% | 0.5M | |||||||||||
| SRR5448117_subsample_1 | 4.5% | 97.8% | 477.2Mb | 9.6M | 50.3% | 96.4% | 0.2% | ||||||||||
| SRR5448118 | 7.0% | 100.0% | 4.3M | IU | 4.8M | 4.7M | 97.7% | 4.3M | 88.4% | 0.4M | |||||||
| SRR5448118_STARpass1 | 4.8M | 4.7M | 97.7% | 4.3M | 88.5% | 0.4M | |||||||||||
| SRR5448118_subsample_1 | 4.2% | 97.8% | 478.6Mb | 9.7M | 50.6% | 96.6% | 0.2% |
Picard
Tools for manipulating high-throughput sequencing data.URL: http://broadinstitute.github.io/picard
Mark Duplicates
Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.
The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.
To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:
READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATESREADS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATESREADS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATESREADS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICALREADS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATESREADS_UNMAPPED = UNMAPPED_READS
Salmon
1.10.2
Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197
STAR
Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635
Summary Statistics
Summary statistics from the STAR alignment
| Sample Name | Total reads | Aligned | Aligned | Uniq aligned | Uniq aligned | Multimapped | Avg. read len | Avg. mapped len | Splices | Annotated splices | GT/AG splices | GC/AG splices | AT/AC splices | Non-canonical splices | Mismatch rate | Del rate | Del len | Ins rate | Ins len |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR5448113 | 4.8M | 4.7M | 98.0% | 4.3M | 87.9% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448113_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 88.0% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448114 | 4.8M | 4.7M | 97.9% | 4.3M | 88.5% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448114_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 88.5% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448115 | 4.8M | 4.7M | 97.9% | 4.2M | 87.8% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448115_STARpass1 | 4.8M | 4.7M | 97.9% | 4.3M | 87.8% | 0.5M | 101.0bp | 101.0bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448116 | 4.8M | 4.7M | 98.0% | 4.3M | 88.8% | 0.4M | 101.0bp | 101.0bp | 1.8M | 1.8M | 1.8M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.2bp |
| SRR5448116_STARpass1 | 4.8M | 4.7M | 98.0% | 4.3M | 88.8% | 0.4M | 101.0bp | 101.0bp | 1.8M | 1.8M | 1.8M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.2bp |
| SRR5448117 | 4.8M | 4.7M | 97.8% | 4.3M | 88.2% | 0.5M | 101.0bp | 100.9bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448117_STARpass1 | 4.8M | 4.7M | 97.8% | 4.3M | 88.2% | 0.5M | 101.0bp | 100.9bp | 1.7M | 1.7M | 1.7M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.5bp | 0.0% | 1.3bp |
| SRR5448118 | 4.8M | 4.7M | 97.7% | 4.3M | 88.4% | 0.4M | 101.0bp | 101.0bp | 1.8M | 1.8M | 1.8M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.6bp | 0.0% | 1.3bp |
| SRR5448118_STARpass1 | 4.8M | 4.7M | 97.7% | 4.3M | 88.5% | 0.4M | 101.0bp | 101.0bp | 1.8M | 1.8M | 1.8M | 0.0M | 0.0M | 0.0M | 0.1% | 0.0% | 1.6bp | 0.0% | 1.3bp |
Alignment Scores
fastp
0.23.4
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Salmon | 1.10.2 |
| fastp | 0.23.4 |